Near-optimal probabilistic RNA-seq quantification
We present kallisto, an RNA-seq quantification program that is two orders of magnitude
faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads …
faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads …
A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs
The equivalence of human induced pluripotent stem cells (hiPSCs) and human embryonic
stem cells (hESCs) remains controversial. Here we use genetically matched hESC and …
stem cells (hESCs) remains controversial. Here we use genetically matched hESC and …
Differential expression analysis of RNA-seq reads: overview, taxonomy, and tools
HA Chowdhury, DK Bhattacharyya… - IEEE/ACM transactions …, 2018 - ieeexplore.ieee.org
Analysis of RNA-sequence (RNA-seq) data is widely used in transcriptomic studies and it
has many applications. We review RNA-seq data analysis from RNA-seq reads to the results …
has many applications. We review RNA-seq data analysis from RNA-seq reads to the results …
Quantitative analysis of high‐throughput biological data
The study of multiple “omes,” such as the genome, transcriptome, proteome, and
metabolome has become widespread in biomedical research. High‐throughput techniques …
metabolome has become widespread in biomedical research. High‐throughput techniques …
Understanding the Role of the WRKY Gene Family under Stress Conditions in Pigeonpea (Cajanus Cajan L.)
Pigeonpea (Cajanus cajan L.), a protein-rich legume, is a major food component of the daily
diet for residents in semi-arid tropical regions of the word. Pigeonpea is also known for its …
diet for residents in semi-arid tropical regions of the word. Pigeonpea is also known for its …
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
Most methods for statistical analysis of RNA-seq data take a matrix of abundance estimates
for some type of genomic features as their input, and consequently the quality of any …
for some type of genomic features as their input, and consequently the quality of any …
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells
Motivation Quantification of isoform abundance has been extensively studied at the mature
RNA level using RNA-seq but not at the level of precursor RNAs using nascent RNA …
RNA level using RNA-seq but not at the level of precursor RNAs using nascent RNA …
VERSE: a versatile and efficient RNA-Seq read counting tool
Motivation RNA-Seq is a powerful technology that delivers digital gene expression data. To
measure expression strength at the gene level, one popular approach is direct read …
measure expression strength at the gene level, one popular approach is direct read …
The genetic basis and evolution of red blood cell sickling in deer
A Esin, LT Bergendahl, V Savolainen… - Nature ecology & …, 2018 - nature.com
Crescent-shaped red blood cells, the hallmark of sickle-cell disease, present a striking
departure from the biconcave disc shape normally found in mammals. Characterized by …
departure from the biconcave disc shape normally found in mammals. Characterized by …
Multidimensional landscape of non‐alcoholic fatty liver disease‐related disease spectrum uncovered by big omics data: Profiling evidence and new perspectives
Z Zhu, Y Chen, X Qin, S Liu, J Wang, H Ren - Smart Medicine, 2023 - Wiley Online Library
Characterized by hepatic lipid accumulation, non‐alcoholic fatty liver disease (NAFLD) is a
multifactorial metabolic disorder that could promote the progression of non‐alcoholic …
multifactorial metabolic disorder that could promote the progression of non‐alcoholic …